Unless the equipment manager or a ballboy fesses up, we'll never know. However, when one looks at the reasons why it may have been done, you'd have to conclude that both Brady and Belicheck knew for two simple reasons.
1. Belicheck's game plan called for the Patriots to run the ball a lot in the first half considering the weather and the perceived threats of the Colt offense. So keep the ball out of the hands of the Colts. To do that, Belicheck would have to find a way to ensure that the Patriots didn't cough the ball up, as they have been prone to do in key games in the past. Best way to do that is to deflate the ball to make it easier to grip and to hang onto.
2. Belicheck would not deflate the balls for 1. above unless it would not adversely affect Brady's passing game. Brady would have to know about it and agree. Considering that Brady has been quoted in the past as favouring a softer, deflated ball and considering that Brady and Manning lobbied the league to reduce the air pressure parameters several years ago, it seems likely that Brady would agree and be on board.